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Chen H, Wang Y, Wang W, Cao T, Zhang L, Wang Z, Chi X, Shi T, Wang H, He X, Liang M, Yang M, Jiang W, Lv D, Yu J, Zhu G, Xie Y, Gao B, Wang X, Liu X, Li Y, Ouyang L, Zhang J, Liu H, Li Z, Tong Y, Xia X, Tan GY, Zhang L. High-yield porphyrin production through metabolic engineering and biocatalysis. Nat Biotechnol 2024:10.1038/s41587-024-02267-3. [PMID: 38839873 DOI: 10.1038/s41587-024-02267-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 04/26/2024] [Indexed: 06/07/2024]
Abstract
Porphyrins and their derivatives find extensive applications in medicine, food, energy and materials. In this study, we produced porphyrin compounds by combining Rhodobacter sphaeroides as an efficient cell factory with enzymatic catalysis. Genome-wide CRISPRi-based screening in R. sphaeroides identifies hemN as a target for improved coproporphyrin III (CPIII) production, and exploiting phosphorylation of PrrA further improves the production of bioactive CPIII to 16.5 g L-1 by fed-batch fermentation. Subsequent screening and engineering high-activity metal chelatases and coproheme decarboxylase results in the synthesis of various metalloporphyrins, including heme and the anti-tumor agent zincphyrin. After pilot-scale fermentation (200 L) and setting up the purification process for CPIII (purity >95%), we scaled up the production of heme and zincphyrin through enzymatic catalysis in a 5-L bioreactor, with CPIII achieving respective enzyme conversion rates of 63% and 98% and yielding 10.8 g L-1 and 21.3 g L-1, respectively. Our strategy offers a solution for high-yield bioproduction of heme and other valuable porphyrins with substantial industrial and medical applications.
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Affiliation(s)
- Haihong Chen
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Yaohong Wang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ting Cao
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Lu Zhang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Zhengduo Wang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Xuran Chi
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Tong Shi
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Huangwei Wang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Xinwei He
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Mindong Liang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Mengxue Yang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Wenyi Jiang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Dongyuan Lv
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Jiaming Yu
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Guoliang Zhu
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Yongtao Xie
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Bei Gao
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Xinye Wang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Youyuan Li
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Liming Ouyang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Jingyu Zhang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Huimin Liu
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Zilong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yaojun Tong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuekui Xia
- Key Biosensor Laboratory of Shandong Province, Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Gao-Yi Tan
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China.
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China.
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Fan J, Xu W, Xu X, Wang Y. Production of Coenzyme Q 10 by microbes: an update. World J Microbiol Biotechnol 2022; 38:194. [PMID: 35984526 DOI: 10.1007/s11274-022-03326-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 05/31/2022] [Indexed: 11/26/2022]
Abstract
Coenzyme Q10 (CoQ10) is the main CoQ species in human and is used extensively in food, cosmetic and medicine industries because of its antioxidant properties and its benefit in prophylactic medicine and therapy for a variety of diseases. Among various approaches to increase the production of CoQ10, microbial fermentation is the most effective. As knowledge of the biosynthetic enzymes and regulatory mechanisms modulating CoQ10 production increases, opportunities arise for metabolic engineering of CoQ10 in microbial hosts. In this review, we present various strategies used up to date to improve CoQ10 production and focus on metabolic engineering of CoQ10 overproduction in microbes. General strategies of metabolic engineering include providing sufficient precursors for CoQ10, increasing metabolic fluxes, and expanding storage capacity for CoQ10. Based on these strategies, CoQ10 production has been significantly improved in natural CoQ10 producers, as well as in heterologous hosts.
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Affiliation(s)
- Jinbo Fan
- Xi'an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an, China
- School of Basic Medicine, Xi'an Medical University, Xi'an, 710021, China
| | - Wen Xu
- Xi'an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an, China
- School of Basic Medicine, Xi'an Medical University, Xi'an, 710021, China
| | - Xi Xu
- School of Basic Medicine, Xi'an Medical University, Xi'an, 710021, China.
| | - Yang Wang
- Xi'an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an, China.
- School of Basic Medicine, Xi'an Medical University, Xi'an, 710021, China.
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Zhang L, Li YL, Hu JH, Liu ZY. Overexpression of enzymes in glycolysis and energy metabolic pathways to enhance coenzyme Q10 production in Rhodobacter sphaeroides VK-2-3. Front Microbiol 2022; 13:931470. [PMID: 36033867 PMCID: PMC9412181 DOI: 10.3389/fmicb.2022.931470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/26/2022] [Indexed: 12/02/2022] Open
Abstract
We subjected the components of the glycolysis and energy metabolism pathways of Rhodobacter sphaeroides (R. sphaeroides) to metabolic engineering to improve the titer and yield of coenzyme Q10 (CoQ10). Phosphofructokinase (PFK), cyclic adenylate-dependent protein kinase (PKAC), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and adenosine triphosphate hydrolase (KdpC) were overexpressed in R. sphaeroides VK-2-3 (VK-2-3). The strains were labeled R. sphaeroides PFK (RS.PFK), RS.PKAC, RS.PFK–PKAC, RS.KdpC, RS.GAPDH, and RS.KdpC–GAPDH. Results showed that the CoQ10 titers of RS.PFK, RS.PKAC, and RS.PFK–PKAC were 300.96 ± 0.87, 405.94 ± 4.77, and 379.94 ± 0.42 mg/l, respectively. The CoQ10 titers of RS.PFK and VK-2-3 were not significantly different; however, those for RS.PKAC and RS.PFK–PKAC were 13 and 6% higher than that of VK-2-3, respectively. Further, the titers of RS.KdpC, RS.GAPDH, and RS.KdpC–GAPDH were 360.17 ± 0.39, 409.79 ± 0.76, and 359.87 ± 1.14 mg/l, respectively. The titers of RS.KdpC and RS.KdpC–GAPDH were not significantly different from that for VK-2-3, whereas that for RS.GAPDH was 14% higher than that of VK-2-3. Finally, when the cultures of RS.GAPDH and VK-2-3 were scaled up in 5-L fermenters, the CoQ10 titers and RS.GAPDH yields increased by 44.3 and 37.8%, respectively, compared with VK-2-3.To the best of our knowledge, the glycolysis pathway of R. sphaeroides was studied for the first time in this study. We genetically modified the components of the energy metabolism pathway to obtain the strain with high yield of CoQ10 mutant RS.GAPDH. The findings of this study can serve as a basis for future studies involving metabolic engineering of CoQ10-producing strains.
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Affiliation(s)
- Long Zhang
- Inner Mongolia Energy Conservation and Emission Reduction Engineering Technology Research Center for Fermentation Industry, Hohhot, Inner Mongolia, China
- Engineering Research Center of Inner Mongolia for Green Manufacturing in Bio-fermentation Industry, Hohhot, Inner Mongolia, China
- College of Chemical Engineering, Inner Mongolia University of Technology, Hohhot, Inner Mongolia, China
| | - Yong-li Li
- Inner Mongolia Energy Conservation and Emission Reduction Engineering Technology Research Center for Fermentation Industry, Hohhot, Inner Mongolia, China
- Engineering Research Center of Inner Mongolia for Green Manufacturing in Bio-fermentation Industry, Hohhot, Inner Mongolia, China
- College of Chemical Engineering, Inner Mongolia University of Technology, Hohhot, Inner Mongolia, China
| | - Jian-hua Hu
- Inner Mongolia Energy Conservation and Emission Reduction Engineering Technology Research Center for Fermentation Industry, Hohhot, Inner Mongolia, China
- Engineering Research Center of Inner Mongolia for Green Manufacturing in Bio-fermentation Industry, Hohhot, Inner Mongolia, China
- College of Chemical Engineering, Inner Mongolia University of Technology, Hohhot, Inner Mongolia, China
| | - Zhan-ying Liu
- Inner Mongolia Energy Conservation and Emission Reduction Engineering Technology Research Center for Fermentation Industry, Hohhot, Inner Mongolia, China
- Engineering Research Center of Inner Mongolia for Green Manufacturing in Bio-fermentation Industry, Hohhot, Inner Mongolia, China
- College of Chemical Engineering, Inner Mongolia University of Technology, Hohhot, Inner Mongolia, China
- *Correspondence: Zhan-ying Liu,
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Mitra S, Dhar R, Sen R. Designer bacterial cell factories for improved production of commercially valuable non-ribosomal peptides. Biotechnol Adv 2022; 60:108023. [PMID: 35872292 DOI: 10.1016/j.biotechadv.2022.108023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/30/2022] [Accepted: 07/18/2022] [Indexed: 11/27/2022]
Abstract
Non-ribosomal peptides have gained significant attention as secondary metabolites of high commercial importance. This group houses a diverse range of bioactive compounds, ranging from biosurfactants to antimicrobial and cytotoxic agents. However, low yield of synthesis by bacteria and excessive losses during purification hinders the industrial-scale production of non-ribosomal peptides, and subsequently limits their widespread applicability. While isolation of efficient producer strains and optimization of bioprocesses have been extensively used to enhance yield, further improvement can be made by optimization of the microbial strain using the tools and techniques of metabolic engineering, synthetic biology, systems biology, and adaptive laboratory evolution. These techniques, which directly target the genome of producer strains, aim to redirect carbon and nitrogen fluxes of the metabolic network towards the desired product, bypass the feedback inhibition and repression mechanisms that limit the maximum productivity of the strain, and even extend the substrate range of the cell for synthesis of the target product. The present review takes a comprehensive look into the biosynthesis of bacterial NRPs, how the same is regulated by the cell, and dives deep into the strategies that have been undertaken for enhancing the yield of NRPs, while also providing a perspective on other potential strategies that can allow for further yield improvement. Furthermore, this review provides the reader with a holistic perspective on the design of cellular factories of NRP production, starting from general techniques performed in the laboratory to the computational techniques that help a biochemical engineer model and subsequently strategize the architectural plan.
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Affiliation(s)
- Sayak Mitra
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Riddhiman Dhar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India.
| | - Ramkrishna Sen
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India.
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5
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Rational Engineering of Non-Ubiquinone Containing Corynebacterium glutamicum for Enhanced Coenzyme Q10 Production. Metabolites 2022; 12:metabo12050428. [PMID: 35629932 PMCID: PMC9145305 DOI: 10.3390/metabo12050428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 11/17/2022] Open
Abstract
Coenzyme Q10 (CoQ10) is a lipid-soluble compound with important physiological functions and is sought after in the food and cosmetic industries owing to its antioxidant properties. In our previous proof of concept, we engineered for CoQ10 biosynthesis the industrially relevant Corynebacterium glutamicum, which does not naturally synthesize any CoQ. Here, liquid chromatography–mass spectrometry (LC–MS) analysis identified two metabolic bottlenecks in the CoQ10 production, i.e., low conversion of the intermediate 10-prenylphenol (10P-Ph) to CoQ10 and the accumulation of isoprenologs with prenyl chain lengths of not only 10, but also 8 to 11 isopentenyl units. To overcome these limitations, the strain was engineered for expression of the Ubi complex accessory factors UbiJ and UbiK from Escherichia coli to increase flux towards CoQ10, and by replacement of the native polyprenyl diphosphate synthase IspB with a decaprenyl diphosphate synthase (DdsA) to select for prenyl chains with 10 isopentenyl units. The best strain UBI6-Rs showed a seven-fold increased CoQ10 content and eight-fold increased CoQ10 titer compared to the initial strain UBI4-Pd, while the abundance of CoQ8, CoQ9, and CoQ11 was significantly reduced. This study demonstrates the application of the recent insight into CoQ biosynthesis to improve metabolic engineering of a heterologous CoQ10 production strain.
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Zhu Y, Pan M, Wang C, Ye L, Xia C, Yu H. Enhanced CoQ10 production by genome modification of Rhodobacter sphaeroides via Tn7 transposition. FEMS Microbiol Lett 2022; 369:6537402. [PMID: 35218188 DOI: 10.1093/femsle/fnab160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/31/2021] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
As a native CoQ10 producer, Rhodobacter sphaeroides has been extensively engineered to enhance CoQ10 production. However, the genetic manipulations using plasmids suffer from risk of plasmid loss during propagation process, biomass impairment due to cellular burden and bio-safety concerns. In this paper, genomic manipulations via Tn7 transposition was conducted to boost the CoQ10 biosynthesis in R. sphaeroides. The titer production and content of CoQ10 were improved by 18.44% and 18.87% respectively compared to the wild type, when an additional copy of dxs and dxr were integrated into the genome. Further overexpression of idi and ispD by genomic integration created strain RSPCDDII with CoQ10 production and content of 81.23 mg/L and 5.93 mg/g, which were 54.28% and 55.97% higher than those of the wild type. The gene segments were successfully inserted into the attTn7 site of the R. sphaeroides genome. Meanwhile, the biomass was not affected. Compared to overexpression of genes on plasmids, this strategy could enhance protein expression to a proper level without affecting cell growth, and in a more stable manner.
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Affiliation(s)
- Yongqiang Zhu
- Institute of Materials Engineering, Suqian University, Suqian 223800, PR China.,Group of Bioengineering, ZheJiang NHU Company Limited, Shaoxing 312521, PR China.,Institute of Bioengineering, Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Mengyao Pan
- Group of Bioengineering, ZheJiang NHU Company Limited, Shaoxing 312521, PR China
| | - Chenfei Wang
- Group of Bioengineering, ZheJiang NHU Company Limited, Shaoxing 312521, PR China
| | - Lidan Ye
- Institute of Bioengineering, Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Chunmiao Xia
- Anhui Laboratory of Clean Energy Materials and Chemistry for Sustainable Conversion of Natural Resources, School of Chemical and Environmental Engineering, Anhui Polytechnic University, Wuhu 241000, PR China
| | - Hongwei Yu
- Institute of Bioengineering, Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China
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Pierrel F, Burgardt A, Lee JH, Pelosi L, Wendisch VF. Recent advances in the metabolic pathways and microbial production of coenzyme Q. World J Microbiol Biotechnol 2022; 38:58. [PMID: 35178585 PMCID: PMC8854274 DOI: 10.1007/s11274-022-03242-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/30/2022] [Indexed: 12/13/2022]
Abstract
Coenzyme Q (CoQ) serves as an electron carrier in aerobic respiration and has become an interesting target for biotechnological production due to its antioxidative effect and benefits in supplementation to patients with various diseases. Here, we review discovery of the pathway with a particular focus on its superstructuration and regulation, and we summarize the metabolic engineering strategies for overproduction of CoQ by microorganisms. Studies in model microorganisms elucidated the details of CoQ biosynthesis and revealed the existence of multiprotein complexes composed of several enzymes that catalyze consecutive reactions in the CoQ pathways of Saccharomyces cerevisiae and Escherichia coli. Recent findings indicate that the identity and the total number of proteins involved in CoQ biosynthesis vary between species, which raises interesting questions about the evolution of the pathway and could provide opportunities for easier engineering of CoQ production. For the biotechnological production, so far only microorganisms have been used that naturally synthesize CoQ10 or a related CoQ species. CoQ biosynthesis requires the aromatic precursor 4-hydroxybenzoic acid and the prenyl side chain that defines the CoQ species. Up to now, metabolic engineering strategies concentrated on the overproduction of the prenyl side chain as well as fine-tuning the expression of ubi genes from the ubiquinone modification pathway, resulting in high CoQ yields. With expanding knowledge about CoQ biosynthesis and exploration of new strategies for strain engineering, microbial CoQ production is expected to improve.
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Affiliation(s)
- Fabien Pierrel
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000, Grenoble, France.
| | - Arthur Burgardt
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jin-Ho Lee
- Department of Food Science & Biotechnology, Kyungsung University, Busan, South Korea
| | - Ludovic Pelosi
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000, Grenoble, France
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
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Liu Q, Lin B, Tao Y. Improved methylation in E. coli via an efficient methyl supply system driven by betaine. Metab Eng 2022; 72:46-55. [DOI: 10.1016/j.ymben.2022.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 01/28/2022] [Accepted: 02/16/2022] [Indexed: 12/21/2022]
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Chen M, Li M, Ye L, Yu H. Construction of Canthaxanthin-Producing Yeast by Combining Spatiotemporal Regulation and Pleiotropic Drug Resistance Engineering. ACS Synth Biol 2022; 11:325-333. [PMID: 34927424 DOI: 10.1021/acssynbio.1c00437] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ketocarotenoid canthaxanthin has important applications in the feed industry. Its biosynthesis using microbial cell factories is an attractive alternative to the current chemical synthesis route. Canthaxanthin-producing Saccharomyces cerevisiae was constructed by introducing the β-carotene ketolase variant OBKTM29 into a β-carotene producer. Subcellular re-localization of OBKTM29 was explored, together with copy number adjustment both in the cytoplasm and on the periplasmic membrane, to accelerate the conversion of β-carotene to canthaxanthin. Moreover, pleiotropic drug resistance (PDR) regulators Pdr1 and Pdr3 were overexpressed to improve the stress tolerance of the yeast strain, leading to obviously enhanced canthaxanthin production. The synthetic pathway was then regulated by a temperature-responsive GAL system to separate product synthesis from cell growth. Finally, 1.44 g/L canthaxanthin was harvested in fed-batch fermentation. This work demonstrated the power of spatial and temporal regulation and the efficiency of PDR engineering in heterologous biosynthesis.
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Affiliation(s)
- Mingkai Chen
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Min Li
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Lidan Ye
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Hongwei Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
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Screening and engineering of high-activity promoter elements through transcriptomics and red fluorescent protein visualization in Rhodobacter sphaeroides. Synth Syst Biotechnol 2021; 6:335-342. [PMID: 34738044 PMCID: PMC8531756 DOI: 10.1016/j.synbio.2021.09.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 12/03/2022] Open
Abstract
The versatile photosynthetic α-proteobacterium Rhodobacter sphaeroides, has recently been extensively engineered as a novel microbial cell factory (MCF) to produce pharmaceuticals, nutraceuticals, commodity chemicals and even hydrogen. However, there are no well-characterized high-activity promoters to modulate gene transcription during the engineering of R. sphaeroides. In this study, several native promoters from R. sphaeroides JDW-710 (JDW-710), an industrial strain producing high levels of co-enzyme Q10 (Q10) were selected on the basis of transcriptomic analysis. These candidate promoters were then characterized by using gusA as a reporter gene. Two native promoters, Prsp_7571 and Prsp_6124, showed 620% and 800% higher activity, respectively, than the tac promoter, which has previously been used for gene overexpression in R. sphaeroides. In addition, a Prsp_7571-derived synthetic promoter library with strengths ranging from 54% to 3200% of that of the tac promoter, was created on the basis of visualization of red fluorescent protein (RFP) expression in R. sphaeroides. Finally, as a demonstration, the synthetic pathway of Q10 was modulated by the selected promoter T334* in JDW-710; the Q10 yield in shake-flasks increased 28% and the production reached 226 mg/L. These well-characterized promoters should be highly useful in current synthetic biology platforms for refactoring the biosynthetic pathway in R. sphaeroides-derived MCFs.
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Bian Q, Zhou P, Yao Z, Li M, Yu H, Ye L. Heterologous biosynthesis of lutein in S. cerevisiae enabled by temporospatial pathway control. Metab Eng 2021; 67:19-28. [PMID: 34077803 DOI: 10.1016/j.ymben.2021.05.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/28/2021] [Accepted: 05/25/2021] [Indexed: 01/09/2023]
Abstract
The market-expanding lutein is currently mainly supplied by plant extraction, with microbial fermentation using engineered cell factory emerging as a promising substitution. During construction of lutein-producing yeast, α-carotene formation through asymmetric ε- and β-cyclization of lycopene was found as the main limiting step, attributed to intra-pathway competition of the cyclases for lycopene, forming β-carotene instead. To solve this problem, temperature-responsive expression of β-cyclase was coupled to constitutive expression of ε-cyclase for flux redirection to α-carotene by allowing ε-cyclization to occur first. Meanwhile, the ε-cyclase was engineered and re-localized to the plasma membrane for further flux reinforcement towards α-carotene. Finally, pathway extension with proper combination of carotenoid hydroxylases enabled lutein (438 μg/g dry cells) biosynthesis in S. cerevisiae. The success of heterologous lutein biosynthesis in yeast suggested temporospatial pathway control as a potential strategy in solving intra-pathway competitions, and may also be applicable for promoting the biosynthesis of other natural products.
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Affiliation(s)
- Qi Bian
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Pingping Zhou
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
| | - Zhen Yao
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Min Li
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Hongwei Yu
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Lidan Ye
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
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Xu W, Ma X, Yao J, Wang D, Li W, Liu L, Shao L, Wang Y. Increasing coenzyme Q 10 yield from Rhodopseudomonas palustris by expressing rate-limiting enzymes and blocking carotenoid and hopanoid pathways. Lett Appl Microbiol 2021; 73:88-95. [PMID: 33783839 DOI: 10.1111/lam.13479] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 11/29/2022]
Abstract
Coenzyme Q10 (CoQ10 ), a strong antioxidant, is used extensively in food, cosmetic and medicine industries. A natural producer, Rhodopseudomonas palustris, was engineered to overproduce CoQ10 . For increasing the CoQ10 content, crtB gene was deleted to block the carotenoid pathway. crtB gene deletion led to 33% improvement of CoQ10 content over the wild type strain. However, it was found that the yield of hopanoids was also increased by competing for the precursors from carotenoid pathway with CoQ10 pathway. To further increase the CoQ10 content, hopanoid pathway was blocked by deleting shc gene, resulting in R. palustris [Δshc, ΔcrtB] to produce 4·7 mg g-1 DCW CoQ10 , which was 1·2 times higher than the CoQ10 content in the wild type strain. The common strategy of co-expression of rate-limiting enzymes (DXS, DPS and UbiA) was combined with the pathway blocking method resulted in 8·2 mg g-1 DCW of CoQ10 , which was 2·9 times higher than that of wild type strain. The results suggested a synergistic effect among different metabolic engineering strategies. This study demonstrates the potential of R. palustris for CoQ10 production and provides viable strategies to increase CoQ10 titer.
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Affiliation(s)
- W Xu
- The Xi'an key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, Shaanxi, China
| | - X Ma
- The Xi'an key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, Shaanxi, China
| | - J Yao
- The Xi'an key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, Shaanxi, China
| | - D Wang
- Department of Prosthodontics, School of Stomatology, Xi'an Medical University, Xi'an, Shaanxi, China
| | - W Li
- The Xi'an key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, Shaanxi, China
| | - Li Liu
- The Xi'an key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, Shaanxi, China
| | - L Shao
- The Xi'an key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, Shaanxi, China
| | - Y Wang
- The Xi'an key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, Shaanxi, China
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Gao Q, Chen H, Wang G, Yang W, Zhong X, Liu J, Huo X, Liu W, Huang J, Tao Y, Lin B. Highly Efficient Production of Menaquinone-7 from Glucose by Metabolically Engineered Escherichia coli. ACS Synth Biol 2021; 10:756-765. [PMID: 33755417 DOI: 10.1021/acssynbio.0c00568] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Menaquinone-7 (MK-7) possesses wide health and medical value, and the market demand for MK-7 has increased. Metabolic engineering for MK-7 production in Escherichia coli still remains challenging due to the characteristics of the competing quinone synthesis, and cells mainly synthesized menaquinones under anaerobic conditions. To increase the production of MK-7 in engineered E. coli strains under aerobic conditions, we divided the whole MK-7 biosynthetic pathway into three modules (MVA pathway, DHNA pathway, and MK-7 pathway) and systematically optimized each of them. First, by screening and enhancing Idi expression, the amounts of MK-7/DMK-7 increased significantly. Then, in the MK-7 pathway, by combinatorial overexpression of endogenous MenA and exogenous UbiE, and fine-tuning the expression of HepPPS, MenA, and UbiE, 70 μM MK-7 was achieved. Third, the DHNA synthetic pathway was enhanced, and 157 μM MK-7 was achieved. By the combinational metabolic engineering strategies and membrane engineering, an efficient metabolic engineered E. coli strain for MK-7 synthesis was developed, and 200 μM (129 mg/L) MK-7 was obtained in shake flask experiment, representing a 306-fold increase compared to the starting strain. In the scale-up fermentation, 2074 μM (1350 mg/L) MK-7 was achieved after 52 h fermentation with a productivity of 26 mg/L/h. This is the highest titer of MK-7 ever reported. This study offers an alternative method for MK-7 production from biorenewable feedstock (glucose) by engineered E. coli. The high titer of our process should make it a promising cost-effective resource for MK-7.
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Affiliation(s)
- Quanxiu Gao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- National Engineering Research Center of Industrial Microbiology and Fermentation Technology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Hao Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gaoyan Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Yang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaotong Zhong
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiezheng Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - XiaoJing Huo
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- National Engineering Research Center of Industrial Microbiology and Fermentation Technology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Weifeng Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianzhong Huang
- National Engineering Research Center of Industrial Microbiology and Fermentation Technology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baixue Lin
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
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14
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Qu Y, Su A, Li Y, Meng Y, Chen Z. Manipulation of the Regulatory Genes ppsR and prrA in Rhodobacter sphaeroides Enhances Lycopene Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:4134-4143. [PMID: 33813825 DOI: 10.1021/acs.jafc.0c08158] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Rhodobacter sphaeroides is a non-sulfur purple bacterium with great metabolic versatility, capable of producing a variety of valuable compounds that include carotenoids and CoQ10. In order to enhance lycopene production, we deleted the photosynthetic gene cluster repressor ppsR from a lycopene-producing Rb. sphaeroides strain (RL1) constructed in a previous study to break the control of carotenoid synthesis by the oxygen level. Also, lycopene production was further increased by overexpression of the activator prrA. The superior lycopene producer DppsR/OprrA thus obtained had a high growth rate and a lycopene production of 150.15 mg/L with a yield of 21.45 mg/g dry cell weight (DCW) under high oxygen conditions; these values were ≥6.85-fold higher than those of RL1 (19.13 mg/L; 3.32 mg/g DCW). Our findings indicate that elimination of oxygen repression led to more efficient lycopene production by DppsR/OprrA and that its increased productivity under high oxygen conditions makes it a potentially useful strain for industrial-scale lycopene production.
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Affiliation(s)
- Yuling Qu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Anping Su
- Shaanxi Engineering Laboratory for Food Green Processing and Security Control, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Ying Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yonghong Meng
- Shaanxi Engineering Laboratory for Food Green Processing and Security Control, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Zhi Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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15
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Burgardt A, Moustafa A, Persicke M, Sproß J, Patschkowski T, Risse JM, Peters-Wendisch P, Lee JH, Wendisch VF. Coenzyme Q 10 Biosynthesis Established in the Non-Ubiquinone Containing Corynebacterium glutamicum by Metabolic Engineering. Front Bioeng Biotechnol 2021; 9:650961. [PMID: 33859981 PMCID: PMC8042324 DOI: 10.3389/fbioe.2021.650961] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Coenzyme Q10 (CoQ10) serves as an electron carrier in aerobic respiration and has become an interesting target for biotechnological production due to its antioxidative effect and benefits in supplementation to patients with various diseases. For the microbial production, so far only bacteria have been used that naturally synthesize CoQ10 or a related CoQ species. Since the whole pathway involves many enzymatic steps and has not been fully elucidated yet, the set of genes required for transfer of CoQ10 synthesis to a bacterium not naturally synthesizing CoQ species remained unknown. Here, we established CoQ10 biosynthesis in the non-ubiquinone-containing Gram-positive Corynebacterium glutamicum by metabolic engineering. CoQ10 biosynthesis involves prenylation and, thus, requires farnesyl diphosphate as precursor. A carotenoid-deficient strain was engineered to synthesize an increased supply of the precursor molecule farnesyl diphosphate. Increased farnesyl diphosphate supply was demonstrated indirectly by increased conversion to amorpha-4,11-diene. To provide the first CoQ10 precursor decaprenyl diphosphate (DPP) from farnesyl diphosphate, DPP synthase gene ddsA from Paracoccus denitrificans was expressed. Improved supply of the second CoQ10 precursor, para-hydroxybenzoate (pHBA), resulted from metabolic engineering of the shikimate pathway. Prenylation of pHBA with DPP and subsequent decarboxylation, hydroxylation, and methylation reactions to yield CoQ10 was achieved by expression of ubi genes from Escherichia coli. CoQ10 biosynthesis was demonstrated in shake-flask cultivation and verified by liquid chromatography mass spectrometry analysis. To the best of our knowledge, this is the first report of CoQ10 production in a non-ubiquinone-containing bacterium.
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Affiliation(s)
- Arthur Burgardt
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Ayham Moustafa
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Marcus Persicke
- Technology Platform Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jens Sproß
- Industrial Organic Chemistry and Biotechnology, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Thomas Patschkowski
- Technology Platform Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Joe Max Risse
- Fermentation Technology, Technical Faculty and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Petra Peters-Wendisch
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jin-Ho Lee
- Major in Food Science & Biotechnology, School of Food Biotechnology & Nutrition, Kyungsung University, Busan, South Korea
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
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16
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Orsi E, Beekwilder J, Eggink G, Kengen SWM, Weusthuis RA. The transition of Rhodobacter sphaeroides into a microbial cell factory. Biotechnol Bioeng 2020; 118:531-541. [PMID: 33038009 PMCID: PMC7894463 DOI: 10.1002/bit.27593] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/29/2020] [Accepted: 10/09/2020] [Indexed: 12/11/2022]
Abstract
Microbial cell factories are the workhorses of industrial biotechnology and improving their performances can significantly optimize industrial bioprocesses. Microbial strain engineering is often employed for increasing the competitiveness of bio‐based product synthesis over more classical petroleum‐based synthesis. Recently, efforts for strain optimization have been standardized within the iterative concept of “design‐build‐test‐learn” (DBTL). This approach has been successfully employed for the improvement of traditional cell factories like Escherichia coli and Saccharomyces cerevisiae. Within the past decade, several new‐to‐industry microorganisms have been investigated as novel cell factories, including the versatile α‐proteobacterium Rhodobacter sphaeroides. Despite its history as a laboratory strain for fundamental studies, there is a growing interest in this bacterium for its ability to synthesize relevant compounds for the bioeconomy, such as isoprenoids, poly‐β‐hydroxybutyrate, and hydrogen. In this study, we reflect on the reasons for establishing R. sphaeroides as a cell factory from the perspective of the DBTL concept. Moreover, we discuss current and future opportunities for extending the use of this microorganism for the bio‐based economy. We believe that applying the DBTL pipeline for R. sphaeroides will further strengthen its relevance as a microbial cell factory. Moreover, the proposed use of strain engineering via the DBTL approach may be extended to other microorganisms that have not been critically investigated yet for industrial applications.
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Affiliation(s)
- Enrico Orsi
- Bioprocess Engineering, Wageningen University, Wageningen, The Netherlands.,Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Gerrit Eggink
- Bioprocess Engineering, Wageningen University, Wageningen, The Netherlands.,Wageningen Food and Biobased Research, Wageningen, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Ruud A Weusthuis
- Bioprocess Engineering, Wageningen University, Wageningen, The Netherlands
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17
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Orsi E, Beekwilder J, van Gelder D, van Houwelingen A, Eggink G, Kengen SW, Weusthuis RA. Functional replacement of isoprenoid pathways in Rhodobacter sphaeroides. Microb Biotechnol 2020; 13:1082-1093. [PMID: 32207882 PMCID: PMC7264872 DOI: 10.1111/1751-7915.13562] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/30/2020] [Accepted: 03/02/2020] [Indexed: 01/09/2023] Open
Abstract
Advances in synthetic biology and metabolic engineering have proven the potential of introducing metabolic by-passes within cell factories. These pathways can provide a more efficient alternative to endogenous counterparts due to their insensitivity to host's regulatory mechanisms. In this work, we replaced the endogenous essential 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway for isoprenoid biosynthesis in the industrially relevant bacterium Rhodobacter sphaeroides by an orthogonal metabolic route. The native 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway was successfully replaced by a heterologous mevalonate (MVA) pathway from a related bacterium. The functional replacement was confirmed by analysis of the reporter molecule amorpha-4,11-diene after cultivation with [4-13 C]glucose. The engineered R. sphaeroides strain relying exclusively on the MVA pathway was completely functional in conditions for sesquiterpene production and, upon increased expression of the MVA enzymes, it reached even higher sesquiterpene yields than the control strain coexpressing both MEP and MVA modules. This work represents an example where substitution of an essential biochemical pathway by an alternative, heterologous pathway leads to enhanced biosynthetic performance.
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Affiliation(s)
- Enrico Orsi
- Bioprocess EngineeringWageningen University6708PBWageningenThe Netherlands
| | | | - Dewi van Gelder
- Bioprocess EngineeringWageningen University6708PBWageningenThe Netherlands
| | | | - Gerrit Eggink
- Bioprocess EngineeringWageningen University6708PBWageningenThe Netherlands
- Wageningen Food and Biobased Research6708WGWageningenThe Netherlands
| | - Servé W.M. Kengen
- Laboratory of MicrobiologyWageningen University6708WEWageningenThe Netherlands
| | - Ruud A. Weusthuis
- Bioprocess EngineeringWageningen University6708PBWageningenThe Netherlands
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18
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Oxygen Uptake Rate Controlling Strategy Balanced with Oxygen Supply for Improving Coenzyme Q10 Production by Rhodobacter sphaeroides. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0461-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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19
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Luo Y, Ge M, Wang B, Sun C, Wang J, Dong Y, Xi JJ. CRISPR/Cas9-deaminase enables robust base editing in Rhodobacter sphaeroides 2.4.1. Microb Cell Fact 2020; 19:93. [PMID: 32334589 PMCID: PMC7183636 DOI: 10.1186/s12934-020-01345-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/02/2020] [Indexed: 12/17/2022] Open
Abstract
Background CRISPR/Cas9 systems have been repurposed as canonical genome editing tools in a variety of species, but no application for the model strain Rhodobacter sphaeroides 2.4.1 was unveiled. Results Here we showed two kinds of programmable base editing systems, cytosine base editors (CBEs) and adenine base editors (ABEs), generated by fusing endonuclease Cas9 variant to cytosine deaminase PmCDA1 or heterodimer adenine deaminase TadA–TadA*, respectively. Using CBEs, we were able to obtain C-to-T mutation of single and double targets following the first induction step, with the efficiency of up to 97% and 43%; while the second induction step was needed in the case of triple target, with the screening rate of 47%. Using ABEs, we were only able to gain A-to-G mutation of single target after the second induction step, with the screening rate of 30%. Additionally, we performed a knockout analysis to identify the genes responsible for coenzyme Q10 biosynthesis and found that ubiF, ubiA, ubiG, and ubiX to be the most crucial ones. Conclusions Together, CBEs and ABEs serve as alternative methods for genetic manipulation in Rhodobacter sphaeroides and will shed light on the fundamental research of other bacteria that are hard to be directly edited by Cas9-sgRNA.
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Affiliation(s)
- Yufeng Luo
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Mei Ge
- Shanghai Laiyi Center for Biopharmaceutical R&D, 800 Dongchuan Road, Shanghai, 200240, China
| | - Bolun Wang
- Department of Biomedical Engineering, State Key Laboratory of Natural and Biomimetic Drugs, College of Engineering, Peking University, Beijing, 100871, China
| | - Changhong Sun
- Beijing Viewsolid Biotech Co. Ltd, Beijing, 100071, China
| | - Junyi Wang
- Department of Biomedical Engineering, State Key Laboratory of Natural and Biomimetic Drugs, College of Engineering, Peking University, Beijing, 100871, China
| | - Yuyang Dong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive NW, Atlanta, GA, 30332, USA
| | - Jianzhong Jeff Xi
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Molecular Medicine, Peking University, Beijing, 100871, China. .,Department of Biomedical Engineering, State Key Laboratory of Natural and Biomimetic Drugs, College of Engineering, Peking University, Beijing, 100871, China.
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20
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Zhang L, Liu L, Wang KF, Xu L, Zhou L, Wang W, Li C, Xu Z, Shi T, Chen H, Li Y, Xu H, Yang X, Zhu Z, Chen B, Li D, Zhan G, Zhang SL, Zhang LX, Tan GY. Phosphate limitation increases coenzyme Q 10 production in industrial Rhodobacter sphaeroides HY01. Synth Syst Biotechnol 2019; 4:212-219. [PMID: 31890925 PMCID: PMC6909082 DOI: 10.1016/j.synbio.2019.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 12/02/2022] Open
Abstract
Coenzyme Q10 (CoQ10) is an important component of the respiratory chain in humans and some bacteria. As a high-value-added nutraceutical antioxidant, CoQ10 has excellent capacity to prevent cardiovascular disease. The content of CoQ10 in the industrial Rhodobacter sphaeroides HY01 is hundreds of folds higher than normal physiological levels. In this study, we found that overexpression or optimization of the synthetic pathway failed CoQ10 overproduction in the HY01 strain. Moreover, under phosphate- limited conditions (decreased phosphate or in the absence of inorganic phosphate addition), CoQ10 production increased significantly by 12% to220 mg/L, biomass decreased by 12%, and the CoQ10 productivity of unit cells increased by 27%. In subsequent fed-batch fermentation, CoQ10 production reached 272 mg/L in the shake-flask fermentation and 1.95 g/L in a 100-L bioreactor under phosphate limitation. Furthermore, to understand the mechanism associated with CoQ10 overproduction under phosphate- limited conditions, the comparatve transcriptome analysis was performed. These results indicated that phosphate limitation combined with glucose fed-batch fermentation represented an effective strategy for CoQ10 production in the HY01. Phosphate limitation induced a pleiotropic effect on cell metabolism, and that improved CoQ10 biosynthesis efficiency was possibly related to the disturbance of energy metabolism and redox potential.
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Affiliation(s)
- Lu Zhang
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Leshi Liu
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Ke-Feng Wang
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Lan Xu
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), No.1 Beichen West Road, Beijing, 100101, China
| | - Liming Zhou
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), No.1 Beichen West Road, Beijing, 100101, China
| | - Chuan Li
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Zheng Xu
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), No.1 Beichen West Road, Beijing, 100101, China
| | - Tong Shi
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Haihong Chen
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Yuanhang Li
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Hui Xu
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - XiuLiang Yang
- Shandong Jincheng Bio-Pharmaceutical Co., Ltd, No. 117 Qixing River Road, Zibo, 255130, China
| | - Zhichun Zhu
- Inner Mongolia Kingdomway Pharmaceutical Co., Ltd, Tuoketuo Power Industrial Park, Hohhot, 010206, China
| | - Biqin Chen
- Inner Mongolia Kingdomway Pharmaceutical Co., Ltd, Tuoketuo Power Industrial Park, Hohhot, 010206, China
| | - Dan Li
- Inner Mongolia Kingdomway Pharmaceutical Co., Ltd, Tuoketuo Power Industrial Park, Hohhot, 010206, China
| | - Guanghuang Zhan
- Inner Mongolia Kingdomway Pharmaceutical Co., Ltd, Tuoketuo Power Industrial Park, Hohhot, 010206, China
| | - Si-Liang Zhang
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Li-Xin Zhang
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Gao-Yi Tan
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
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21
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Mougiakos I, Orsi E, Ghiffary MR, Post W, de Maria A, Adiego-Perez B, Kengen SWM, Weusthuis RA, van der Oost J. Efficient Cas9-based genome editing of Rhodobacter sphaeroides for metabolic engineering. Microb Cell Fact 2019; 18:204. [PMID: 31767004 PMCID: PMC6876111 DOI: 10.1186/s12934-019-1255-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 11/13/2019] [Indexed: 12/18/2022] Open
Abstract
Background Rhodobacter sphaeroides is a metabolically versatile bacterium that serves as a model for analysis of photosynthesis, hydrogen production and terpene biosynthesis. The elimination of by-products formation, such as poly-β-hydroxybutyrate (PHB), has been an important metabolic engineering target for R. sphaeroides. However, the lack of efficient markerless genome editing tools for R. sphaeroides is a bottleneck for fundamental studies and biotechnological exploitation. The Cas9 RNA-guided DNA-endonuclease from the type II CRISPR-Cas system of Streptococcus pyogenes (SpCas9) has been extensively employed for the development of genome engineering tools for prokaryotes and eukaryotes, but not for R. sphaeroides. Results Here we describe the development of a highly efficient SpCas9-based genomic DNA targeting system for R. sphaeroides, which we combine with plasmid-borne homologous recombination (HR) templates developing a Cas9-based markerless and time-effective genome editing tool. We further employ the tool for knocking-out the uracil phosphoribosyltransferase (upp) gene from the genome of R. sphaeroides, as well as knocking it back in while altering its start codon. These proof-of-principle processes resulted in editing efficiencies of up to 100% for the knock-out yet less than 15% for the knock-in. We subsequently employed the developed genome editing tool for the consecutive deletion of the two predicted acetoacetyl-CoA reductase genes phaB and phbB in the genome of R. sphaeroides. The culturing of the constructed knock-out strains under PHB producing conditions showed that PHB biosynthesis is supported only by PhaB, while the growth of the R. sphaeroides ΔphbB strains under the same conditions is only slightly affected. Conclusions In this study, we combine the SpCas9 targeting activity with the native homologous recombination (HR) mechanism of R. sphaeroides for the development of a genome editing tool. We further employ the developed tool for the elucidation of the PHB production pathway of R. sphaeroides. We anticipate that the presented work will accelerate molecular research with R. sphaeroides.
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Affiliation(s)
- Ioannis Mougiakos
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Enrico Orsi
- Bioprocess Engineering, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Mohammad Rifqi Ghiffary
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.,Bioprocess Engineering, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.,Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Wilbert Post
- Bioprocess Engineering, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Alberto de Maria
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.,Bioprocess Engineering, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.,Systems and Synthetic Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Belén Adiego-Perez
- Bioprocess Engineering, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Ruud A Weusthuis
- Bioprocess Engineering, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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22
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Macías FA, Mejías FJ, Molinillo JM. Recent advances in allelopathy for weed control: from knowledge to applications. PEST MANAGEMENT SCIENCE 2019; 75:2413-2436. [PMID: 30684299 DOI: 10.1002/ps.5355] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/10/2019] [Accepted: 01/19/2019] [Indexed: 05/27/2023]
Abstract
Allelopathy is the biological phenomenon of chemical interactions between living organisms in the ecosystem, and must be taken into account in addressing pest and weed problems in future sustainable agriculture. Allelopathy is a multidisciplinary science, but in some cases, aspects of its chemistry are overlooked, despite the need for a deep knowledge of the chemical structural characteristics of allelochemicals to facilitate the design of new herbicides. This review is focused on the most important advances in allelopathy, paying particular attention to the design and development of phenolic compounds, terpenoids and alkaloids as herbicides. The isolation of allelochemicals is mainly addressed, but other aspects such as the analysis and activities of derivatives or analogs are also covered. Furthermore, the use of allelopathy in the fight against parasitic plants is included. The past 12 years have been a prolific period for publications on allelopathy. This critical review discusses future research areas in this field and the state of the art is analyzed from the chemist's perspective. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Francisco A Macías
- Allelopathy Group, Department of Organic Chemistry, School of Sciences, Institute of Biomolecules (INBIO), University of Cadiz, Cádiz, Spain
| | - Francisco Jr Mejías
- Allelopathy Group, Department of Organic Chemistry, School of Sciences, Institute of Biomolecules (INBIO), University of Cadiz, Cádiz, Spain
| | - José Mg Molinillo
- Allelopathy Group, Department of Organic Chemistry, School of Sciences, Institute of Biomolecules (INBIO), University of Cadiz, Cádiz, Spain
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23
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Qiang S, Su AP, Li Y, Chen Z, Hu CY, Meng YH. Elevated β-Carotene Synthesis by the Engineered Rhodobacter sphaeroides with Enhanced CrtY Expression. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:9560-9568. [PMID: 31368704 DOI: 10.1021/acs.jafc.9b02597] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
β-Carotene is a precursor of vitamin A and a dietary supplement for its antioxidant property. Producing β-carotene by microbial fermentation has attracted much attention owing to consumers' preference for the natural product. In this study, an engineered photosynthetic Rhodobacter sphaeroides producing β-carotene was constructed by the following strategies: (1) five promoters of different strengths were used to investigate the effect of the expression level of crtY on β-carotene content. It was found that PrrnB increased the β-carotene content by 109%. (2) blocking of the branched pentose phosphate pathway by zwf deletion, and (3) overexpressing dxs could restore the transcriptional levels of crtE and crtB. Finally, the engineered RS-C3 has the highest β-carotene content of 14.93 mg/g dry cell weight (DCW) among all of the reported photosynthetic bacteria and the β-carotene content reached 3.34 mg/g DCW under light conditions. Our results will be available for industrial use to supply a large quantity of natural β-carotene.
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Affiliation(s)
- Shan Qiang
- Shaanxi Engineering Lab for Food Green Processing and Security Control, College of Food Engineering and Nutritional Science , Shaanxi Normal University , 620 West Chang'an Avenue , Chang'an, Xi'an 710119 , P. R. China
- Xi'an Healthful Biotechnology Co., Ltd. , HangTuo Road , Chang'an, Xi'an 710100 , P. R. China
| | - An Ping Su
- Shaanxi Engineering Lab for Food Green Processing and Security Control, College of Food Engineering and Nutritional Science , Shaanxi Normal University , 620 West Chang'an Avenue , Chang'an, Xi'an 710119 , P. R. China
| | - Ying Li
- State Key Laboratory of Agrobiotechnology , China Agricultural University , No. 2 Yuanmingyuan West Road , Haidian District, Beijing 100193 , P. R. China
| | - Zhi Chen
- State Key Laboratory of Agrobiotechnology , China Agricultural University , No. 2 Yuanmingyuan West Road , Haidian District, Beijing 100193 , P. R. China
| | - Ching Yuan Hu
- Human Nutrition, Food, and Animal Science , University of Hawai'i at Manoa , 1955 East-West Road, AgSci. 415J , Honolulu , Hawaii 96822-2217 , United States
| | - Yong Hong Meng
- Shaanxi Engineering Lab for Food Green Processing and Security Control, College of Food Engineering and Nutritional Science , Shaanxi Normal University , 620 West Chang'an Avenue , Chang'an, Xi'an 710119 , P. R. China
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24
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Ma Y, McClure DD, Somerville MV, Proschogo NW, Dehghani F, Kavanagh JM, Coleman NV. Metabolic Engineering of the MEP Pathway in Bacillus subtilis for Increased Biosynthesis of Menaquinone-7. ACS Synth Biol 2019; 8:1620-1630. [PMID: 31250633 DOI: 10.1021/acssynbio.9b00077] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Vitamin K is essential for blood coagulation and plays important roles in bone and cardiovascular health. Menaquinone-7 (MK-7) is one form of vitamin K that is especially useful due to its long half-life in the circulation. MK-7 is difficult to make via organic synthesis, and is thus commonly produced by fermentation. This study aimed to genetically modify Bacillus subtilis cultures to increase their MK-7 yield and reduce production costs. We constructed 12 different strains of B. subtilis 168 by overexpressing different combinations of the rate-limiting enzymes Dxs, Dxr, Idi, and MenA. We observed an 11-fold enhancement of production in the best-performing strain, resulting in 50 mg/L MK-7. Metabolite analysis revealed new bottlenecks in the pathway at IspG and IspH, which suggest avenues for further optimization. This work highlights the usefulness of Bacillus subtilis for industrial production of high value compounds.
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Affiliation(s)
- Yanwei Ma
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - Dale D. McClure
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - Mark V. Somerville
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Fariba Dehghani
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - John M. Kavanagh
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - Nicholas V. Coleman
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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25
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Tokuyama K, Toya Y, Shimizu H. Prediction of Rate-Limiting Reactions for Growth-Associated Production Using a Constraint-Based Approach. Biotechnol J 2019; 14:e1800431. [PMID: 31218797 DOI: 10.1002/biot.201800431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 05/29/2019] [Indexed: 11/08/2022]
Abstract
Identification of a rate-limiting step in pathways is a key challenge in metabolic engineering. Although the prediction of rate-limiting steps using a kinetic model is a powerful approach, there are several technical hurdles for developing a kinetic model. In this study, an in silico screening algorithm of key enzyme for metabolic engineering is developed to identify the possible rate-limiting reactions for the growth-coupled target production using a stoichiometric model without any experimental data and kinetic parameters. In this method, for each reaction, an upper-bound flux constraint is imposed and the target production is predicted by linear programming. When the constraint decreases the target production at the optimal growth state, the reaction is thought to be a possible rate-limiting step. For validation, this method is applied to the production of succinate or 1,4-butanediol (1,4-BDO) in Escherichia coli, in which the experimental engineering for eliminating rate-limiting steps has been previously reported. In succinate production from glycerol, nine reactions including phosphoenolpyruvate carboxylase are predicted as the rate-limiting steps. In 1,4-BDO production from glucose, eight reactions including pyruvate dehydrogenase are predicted as the rate-limiting steps. These predictions include experimentally identified rate-limiting steps, which would contribute to metabolic engineering as a practical tool for screening candidates of rate-limiting reactions.
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Affiliation(s)
- Kento Tokuyama
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
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26
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Orsi E, Folch PL, Monje-López VT, Fernhout BM, Turcato A, Kengen SWM, Eggink G, Weusthuis RA. Characterization of heterotrophic growth and sesquiterpene production by Rhodobacter sphaeroides on a defined medium. J Ind Microbiol Biotechnol 2019; 46:1179-1190. [PMID: 31187318 PMCID: PMC6697705 DOI: 10.1007/s10295-019-02201-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/29/2019] [Indexed: 11/30/2022]
Abstract
Rhodobacter sphaeroides is a metabolically versatile bacterium capable of producing terpenes natively. Surprisingly, terpene biosynthesis in this species has always been investigated in complex media, with unknown compounds possibly acting as carbon and nitrogen sources. Here, a defined medium was adapted for R. sphaeroides dark heterotrophic growth, and was used to investigate the conversion of different organic substrates into the reporter terpene amorphadiene. The amorphadiene synthase was cloned in R. sphaeroides, allowing its biosynthesis via the native 2-methyl-d-erythritol-4-phosphate (MEP) pathway and, additionally, via a heterologous mevalonate one. The latter condition increased titers up to eightfold. Consequently, better yields and productivities to previously reported complex media cultivations were achieved. Productivity was further investigated under different cultivation conditions, including nitrogen and oxygen availability. This novel cultivation setup provided useful insight into the understanding of terpene biosynthesis in R. sphaeroides, allowing to better comprehend its dynamics and regulation during chemoheterotrophic cultivation.
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Affiliation(s)
- Enrico Orsi
- Bioprocess Engineering, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands
| | - Pauline L Folch
- Bioprocess Engineering, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands
| | - Vicente T Monje-López
- Bioprocess Engineering, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands
| | - Bas M Fernhout
- Bioprocess Engineering, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands
| | - Alessandro Turcato
- Bioprocess Engineering, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands
| | - Gerrit Eggink
- Bioprocess Engineering, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands.,Biobased Products Food and Biobased Research, Wageningen University and Research, Wageningen, The Netherlands
| | - Ruud A Weusthuis
- Bioprocess Engineering, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands.
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27
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28
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Xu W, Yao J, Liu L, Ma X, Li W, Sun X, Wang Y. Improving squalene production by enhancing the NADPH/NADP + ratio, modifying the isoprenoid-feeding module and blocking the menaquinone pathway in Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:68. [PMID: 30962822 PMCID: PMC6437923 DOI: 10.1186/s13068-019-1415-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/20/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND Squalene is currently used widely in the food, cosmetics, and medicine industries. It could also replace petroleum as a raw material for fuels. Microbial fermentation processes for squalene production have been emerging over recent years. In this study, to study the squalene-producing potential of Escherichia coli (E. coli), we employed several increasing strategies for systematic metabolic engineering. These include the expression of human truncated squalene synthase, the overexpression of rate-limiting enzymes in isoprenoid pathway, the modification of isoprenoid-feeding module and the blocking of menaquinone pathway. RESULTS Herein, human truncated squalene synthase was engineered in Escherichia coli to create a squalene-producing bacterial strain. To increase squalene yield, we employed several metabolic engineering strategies. A fivefold squalene titer increase was achieved by expressing rate-limiting enzymes (IDI, DXS, and FPS) involved in the isoprenoid pathway. Pyridine nucleotide transhydrogenase (UdhA) was then expressed to improve the cellular NADPH/NADP+ ratio, resulting in a 59% increase in squalene titer. The Embden-Meyerhof pathway (EMP) was replaced with the Entner-Doudoroff pathway (EDP) and pentose phosphate pathway (PPP) to feed the isoprenoid pathway, along with the overexpression of zwf and pgl genes which encode rate-limiting enzymes in the EDP and PPP, leading to a 104% squalene content increase. Based on the blocking of menaquinone pathway, a further 17.7% increase in squalene content was achieved. Squalene content reached a final 28.5 mg/g DCW and 52.1 mg/L. CONCLUSIONS This study provided novel strategies for improving squalene yield and demonstrated the potential of producing squalene by E. coli.
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Affiliation(s)
- Wen Xu
- The Molecular Virology and Viral Immunology Laboratory, Xi’an Medical University, Xi’an, 710021 Shaanxi China
| | - Jia Yao
- The Molecular Virology and Viral Immunology Laboratory, Xi’an Medical University, Xi’an, 710021 Shaanxi China
| | - Lijun Liu
- The Molecular Virology and Viral Immunology Laboratory, Xi’an Medical University, Xi’an, 710021 Shaanxi China
| | - Xi Ma
- The Molecular Virology and Viral Immunology Laboratory, Xi’an Medical University, Xi’an, 710021 Shaanxi China
| | - Wei Li
- The Molecular Virology and Viral Immunology Laboratory, Xi’an Medical University, Xi’an, 710021 Shaanxi China
| | - Xiaojing Sun
- The Molecular Virology and Viral Immunology Laboratory, Xi’an Medical University, Xi’an, 710021 Shaanxi China
| | - Yang Wang
- The Molecular Virology and Viral Immunology Laboratory, Xi’an Medical University, Xi’an, 710021 Shaanxi China
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29
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Amara A, Takano E, Breitling R. Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism. BMC Genomics 2018; 19:519. [PMID: 29973148 PMCID: PMC6040156 DOI: 10.1186/s12864-018-4905-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/28/2018] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Streptomyces species produce a vast diversity of secondary metabolites of clinical and biotechnological importance, in particular antibiotics. Recent developments in metabolic engineering, synthetic and systems biology have opened new opportunities to exploit Streptomyces secondary metabolism, but achieving industry-level production without time-consuming optimization has remained challenging. Genome-scale metabolic modelling has been shown to be a powerful tool to guide metabolic engineering strategies for accelerated strain optimization, and several generations of models of Streptomyces metabolism have been developed for this purpose. RESULTS Here, we present the most recent update of a genome-scale stoichiometric constraint-based model of the metabolism of Streptomyces coelicolor, the major model organism for the production of antibiotics in the genus. We show that the updated model enables better metabolic flux and biomass predictions and facilitates the integrative analysis of multi-omics data such as transcriptomics, proteomics and metabolomics. CONCLUSIONS The updated model presented here provides an enhanced basis for the next generation of metabolic engineering attempts in Streptomyces.
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Affiliation(s)
- Adam Amara
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
| | - Eriko Takano
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
| | - Rainer Breitling
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
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30
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Su A, Chi S, Li Y, Tan S, Qiang S, Chen Z, Meng Y. Metabolic Redesign of Rhodobacter sphaeroides for Lycopene Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:5879-5885. [PMID: 29806774 DOI: 10.1021/acs.jafc.8b00855] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Lycopene plays an important role as an antioxidative and anticancer agent, and is an increasingly valuable commodity in the global market. Rhodobacter sphaeroides, a carotenogenic and phototrophic bacterium, is an efficient and practical host for carotenoid production. Herein, we explored the potential of metabolically engineered Rb. sphaeroides as a novel platform to produce lycopene. The basal lycopene-producing strain was generated by introducing an exogenous crtI4 from Rhodospirillum rubrum to replace the native crtI3 and deleting crtC in Rb. sphaeroides. Furthermore, knocking out zwf blocked the competitive pentose phosphate pathway and improved the lycopene content by 88%. Finally, the methylerythritol phosphate pathway was reinforced by integration of dxs combined with zwf deletion, which further increased the lycopene content. The final engineered strain produced lycopene to 10.32 mg/g dry cell weight. This study describes a new lycopene producer and provides insight into a photosynthetic bacterium as a host for lycopene biosynthesis.
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Affiliation(s)
- Anping Su
- Shaanxi Engineering Lab for Food Green Processing and Security Control, College of Food Engineering and Nutritional Science , Shaanxi Normal University , 620 West Chang'an Avenue , Chang'an, Xi'an 710119 , P.R. China
| | - Shuang Chi
- State Key Laboratory of Agrobiotechnology , China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District , Beijing 100193 , P.R. China
| | - Ying Li
- State Key Laboratory of Agrobiotechnology , China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District , Beijing 100193 , P.R. China
| | - Siyuan Tan
- Shaanxi Engineering Lab for Food Green Processing and Security Control, College of Food Engineering and Nutritional Science , Shaanxi Normal University , 620 West Chang'an Avenue , Chang'an, Xi'an 710119 , P.R. China
| | - Shan Qiang
- Xi'an Healthful Biotechnology Co., Ltd., HangTuo Road , Chang'an, Xi'an 710100 , P.R. China
| | - Zhi Chen
- State Key Laboratory of Agrobiotechnology , China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District , Beijing 100193 , P.R. China
| | - Yonghong Meng
- Shaanxi Engineering Lab for Food Green Processing and Security Control, College of Food Engineering and Nutritional Science , Shaanxi Normal University , 620 West Chang'an Avenue , Chang'an, Xi'an 710119 , P.R. China
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31
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Zhu Y, Lu W, Ye L, Chen Z, Hu W, Wang C, Chen J, Yu H. Enhanced synthesis of Coenzyme Q 10 by reducing the competitive production of carotenoids in Rhodobacter sphaeroides. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.03.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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32
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Alleviation of metabolic bottleneck by combinatorial engineering enhanced astaxanthin synthesis in Saccharomyces cerevisiae. Enzyme Microb Technol 2017; 100:28-36. [DOI: 10.1016/j.enzmictec.2017.02.006] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 02/10/2017] [Accepted: 02/10/2017] [Indexed: 11/22/2022]
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33
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Wu J, Zhang X, Xia X, Dong M. A systematic optimization of medium chain fatty acid biosynthesis via the reverse beta-oxidation cycle in Escherichia coli. Metab Eng 2017; 41:115-124. [PMID: 28392294 DOI: 10.1016/j.ymben.2017.03.012] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/15/2017] [Accepted: 03/30/2017] [Indexed: 12/24/2022]
Abstract
Medium-chain fatty acids (MCFAs, 6-10 carbons) are valuable precursors to many industrial biofuels and chemicals, recently engineered reversal of the β-oxidation (r-BOX) cycle has been proposed as a potential platform for efficient synthesis of MCFAs. Previous studies have made many exciting achievements on functionally characterizing four core enzymes of this r-BOX cycle. However, the information about bottleneck nodes in this cycle is elusive. Here, a quantitative assessment of the inherent limitations of this cycle was conducted to capitalize on its potential. The selection of the core β-oxidation reversal enzymes in conjunction with acetyl-CoA synthetase endowed the ability to synthesize about 1g/L MCFAs. Furthermore, a gene dosage experiment was developed to identify two rate-limiting enzymes (acetyl-CoA synthetase and thiolase). The de novo pathway was then separated into two modules at thiolase and MCFA production titer increased to 2.8g/L after evaluating different construct environments. Additionally, the metabolism of host organism was reprogrammed to the desired biochemical product by the clustered regularly interspaced short palindromic repeats interference system, resulted in a final MCFA production of 3.8g/L. These findings described here identified the inherent limitations of r-BOX cycle and further unleashed the lipogenic potential of this cycle, thus paving the way for the development of a bacterial platform for microbial production of high-value oleo-chemicals from low-value carbons in a sustainable and environmentally friendly manner.
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Affiliation(s)
- Junjun Wu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang Road, Nanjing, Jiangsu 210095, China
| | - Xia Zhang
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang Road, Nanjing, Jiangsu 210095, China
| | - Xiudong Xia
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210095, China
| | - Mingsheng Dong
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang Road, Nanjing, Jiangsu 210095, China.
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Zhu Y, Ye L, Chen Z, Hu W, Shi Y, Chen J, Wang C, Li Y, Li W, Yu H. Synergic regulation of redox potential and oxygen uptake to enhance production of coenzyme Q 10 in Rhodobacter sphaeroides. Enzyme Microb Technol 2017; 101:36-43. [PMID: 28433189 DOI: 10.1016/j.enzmictec.2017.03.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/10/2017] [Accepted: 03/12/2017] [Indexed: 11/24/2022]
Abstract
The physiological role of Coenzyme Q10 (CoQ10) as an electron carrier suggests its association with redox potential. Overexpression of glyceraldehyde-3-phosphate dehydrogenase type I (gapA-1) in Rhodobacter sphaeroides elevated the NADH/NAD+ ratio and meanwhile enhanced the CoQ10 content by 58%, but at the sacrifice of biomass. On the other hand, Vitreoscilla hemoglobin was heterologously expressed to enhance the oxygen uptake ability of the cells, leading to 127% improvement of biomass. Subsequent coexpression of gapA-1 and vgb resulted in a CoQ10 titer of 83.24mg/L, representing 71% improvement as compared to the control strain RspMCS. When gapA-1 and vgb genes were co-expressed in a previously created strain RspMQd [1], 163.5mg/L of CoQ10 was produced. Finally, 600mg/L of CoQ10 production was achieved in fed-batch fermentation. These results demonstrated the synergic effect of redox potential regulation and oxygen uptake improvement on enhancing CoQ10 production in R. sphaeroides.
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Affiliation(s)
- Yongqiang Zhu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Lidan Ye
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Zhaofeng Chen
- Group of Bioengineering, ZheJiang NHU Company Limited, Shaoxing 312521, PR China
| | - Weijiang Hu
- Group of Bioengineering, ZheJiang NHU Company Limited, Shaoxing 312521, PR China
| | - Yanghui Shi
- Group of Bioengineering, ZheJiang NHU Company Limited, Shaoxing 312521, PR China
| | - Jianbo Chen
- Group of Bioengineering, ZheJiang NHU Company Limited, Shaoxing 312521, PR China
| | - Chenfei Wang
- Group of Bioengineering, ZheJiang NHU Company Limited, Shaoxing 312521, PR China
| | - Yong Li
- Group of Bioengineering, ZheJiang NHU Company Limited, Shaoxing 312521, PR China
| | - Weifeng Li
- Group of Bioengineering, ZheJiang NHU Company Limited, Shaoxing 312521, PR China
| | - Hongwei Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China.
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Lee SQE, Tan TS, Kawamukai M, Chen ES. Cellular factories for coenzyme Q 10 production. Microb Cell Fact 2017; 16:39. [PMID: 28253886 PMCID: PMC5335738 DOI: 10.1186/s12934-017-0646-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 02/10/2017] [Indexed: 04/20/2023] Open
Abstract
Coenzyme Q10 (CoQ10), a benzoquinone present in most organisms, plays an important role in the electron-transport chain, and its deficiency is associated with various neuropathies and muscular disorders. CoQ10 is the only lipid-soluble antioxidant found in humans, and for this, it is gaining popularity in the cosmetic and healthcare industries. To meet the growing demand for CoQ10, there has been considerable interest in ways to enhance its production, the most effective of which remains microbial fermentation. Previous attempts to increase CoQ10 production to an industrial scale have thus far conformed to the strategies used in typical metabolic engineering endeavors. However, the emergence of new tools in the expanding field of synthetic biology has provided a suite of possibilities that extend beyond the traditional modes of metabolic engineering. In this review, we cover the various strategies currently undertaken to upscale CoQ10 production, and discuss some of the potential novel areas for future research.
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Affiliation(s)
- Sean Qiu En Lee
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Tsu Soo Tan
- School of Chemical & Life Sciences, Nanyang Polytechnic, Singapore, Singapore
| | - Makoto Kawamukai
- Faculty of Life and Environmental Science, Shimane University, Matsue, 690-8504, Japan
| | - Ee Sin Chen
- Department of Biochemistry, National University of Singapore, Singapore, Singapore. .,National University Health System (NUHS), Singapore, Singapore. .,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore. .,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore.
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Xu W, Yuan J, Yang S, Ching CB, Liu J. Programming Saposin-Mediated Compensatory Metabolic Sinks for Enhanced Ubiquinone Production. ACS Synth Biol 2016; 5:1404-1411. [PMID: 27389347 DOI: 10.1021/acssynbio.6b00148] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Microbial synthesis of ubiquinone by fermentation processes has been emerging in recent years. However, as ubiquinone is a primary metabolite that is tightly regulated by the host central metabolism, tweaking the individual pathway components could only result in a marginal improvement on the ubiquinone production. Given that ubiquinone is stored in the lipid bilayer, we hypothesized that introducing additional metabolic sink for storing ubiquinone might improve the CoQ10 production. As human lipid binding/transfer protein saposin B (hSapB) was reported to extract ubiquinone from the lipid bilayer and form the water-soluble complex, hSapB was chosen to build a compensatory metabolic sink for the ubiquinone storage. As a proof-of-concept, hSapB-mediated metabolic sink systems were devised and systematically investigated in the model organism of Escherichia coli. The hSapB-mediated periplasmic sink resulted in more than 200% improvement of CoQ8 over the wild type strain. Further investigation revealed that hSapB-mediated sink systems could also improve the CoQ10 production in a CoQ10-hyperproducing E. coli strain obtained by a modular pathway rewiring approach. As the design principles and the engineering strategies reported here are generalizable to other microbes, compensatory sink systems will be a method of significant interest to the synthetic biology community.
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Affiliation(s)
- Wen Xu
- School
of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, Shannxi, China
- Key
Laboratory of Biomedical Information Engineering of Ministry of Education, Xi’an Jiaotong University, Xi’an 710049, Shannxi, China
| | - Jifeng Yuan
- Department
of Chemical and Biomolecular Engineering, National University of Singapore, 117585 Singapore
- Temasek
Laboratories, National University of Singapore, T-Lab Building 5A, 117411 Singapore
| | - Shuiyun Yang
- School
of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, Shannxi, China
- Key
Laboratory of Biomedical Information Engineering of Ministry of Education, Xi’an Jiaotong University, Xi’an 710049, Shannxi, China
| | - Chi-Bun Ching
- Department
of Chemical and Biomolecular Engineering, National University of Singapore, 117585 Singapore
| | - Jiankang Liu
- School
of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, Shannxi, China
- Key
Laboratory of Biomedical Information Engineering of Ministry of Education, Xi’an Jiaotong University, Xi’an 710049, Shannxi, China
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Payet LA, Leroux M, Willison JC, Kihara A, Pelosi L, Pierrel F. Mechanistic Details of Early Steps in Coenzyme Q Biosynthesis Pathway in Yeast. Cell Chem Biol 2016; 23:1241-1250. [PMID: 27693056 DOI: 10.1016/j.chembiol.2016.08.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 07/20/2016] [Accepted: 08/01/2016] [Indexed: 11/17/2022]
Abstract
Coenzyme Q (Q) is a redox lipid that is central for the energetic metabolism of eukaryotes. The biosynthesis of Q from the aromatic precursor 4-hydroxybenzoic acid (4-HB) is understood fairly well. However, biosynthetic details of how 4-HB is produced from tyrosine remain elusive. Here, we provide key insights into this long-standing biosynthetic problem by uncovering molecular details of the first and last reactions of the pathway in the yeast Saccharomyces cerevisiae, namely the deamination of tyrosine to 4-hydroxyphenylpyruvate by Aro8 and Aro9, and the oxidation of 4-hydroxybenzaldehyde to 4-HB by Hfd1. Inactivation of the HFD1 gene in yeast resulted in Q deficiency, which was rescued by the human enzyme ALDH3A1. This suggests that a similar pathway operates in animals, including humans, and led us to propose that patients with genetically unassigned Q deficiency should be screened for mutations in aldehyde dehydrogenase genes, especially ALDH3A1.
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Affiliation(s)
- Laurie-Anne Payet
- Université Grenoble Alpes, Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble (TIMC-IMAG), 38000 Grenoble, France; Centre National de Recherche Scientifique (CNRS), TIMC-IMAG, 38000 Grenoble, France
| | - Mélanie Leroux
- CEA-Grenoble, DRF-BIG-CBM, UMR5249, 38000 Grenoble, France
| | | | - Akio Kihara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo, Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan
| | - Ludovic Pelosi
- Université Grenoble Alpes, Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble (TIMC-IMAG), 38000 Grenoble, France; Centre National de Recherche Scientifique (CNRS), TIMC-IMAG, 38000 Grenoble, France
| | - Fabien Pierrel
- Université Grenoble Alpes, Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble (TIMC-IMAG), 38000 Grenoble, France; Centre National de Recherche Scientifique (CNRS), TIMC-IMAG, 38000 Grenoble, France.
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